The amino acid methionine universally starts a protein chain in all organisms. Furthermore, the N-terminal protein processing pathway is an essential mechanism found in all organisms. In bacteria, protein synthesis involves the formylation and deformylation of the N-terminal methionine. Initially thought to be exclusively present in prokaryotes, peptide deformylase (E.C. 3.5.1.31) catalyzes the removal of the formyl group from the N-terminal methionine of newly synthesized proteins.
More specifically, two enzymes families (peptide deformylase and methionine amino peptidase) are essential for bacterial growth (Meinnel et al., Biochimie 75:1061–1075 (1993)). Peptide deformylase is required for methionine amino peptidase activity. In the methionine cycle, methionyl tRNA is modified to formyl-methionyl tRNA by methionyl tRNA formyltransferase. Next, the formyl methionine is incorporated into the amino termini of newly synthesized polypeptides. Peptide deformylase, also known as polypeptide deformylase, then deformylates the polypeptide to produce N-methionyl polypeptides. At this point, a majority of proteins lose their N-terminal methionine by methionine amino peptidase to afford the mature peptide and free methionine. The free methionine is subsequently recycled.
Recently, the very first eukaryotic peptide deformylases were identified in Arabidopsis thaliana (Giglione et al., EMBO J. 19(21):5916–5929 (2000)). Their data provides the first evidence that eukaryotes, as well as bacteria, share similar N-terminal protein processing machinery. Using their Arabidopsis thaliana peptide deformylase they were also able to isolate a full-length peptide deformylase from tomato (Lycopersicon esculentum; NCBI General Identification No. 17433049; SEQ ID NO:9). In addition to tomato, a rice (Oryza sativa) putative peptide deformylase can be found in GenBank (NCBI General Identification No. 15290077; SEQ ID NO:10).